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Purpose This paper aims to investigate the entropy generation due to magnetohydrodynamic natural convection flow and heat transfer in a porous enclosure filled with Cu-water nanofluid in the presence of viscous dissipation effect. The left and right walls of the cavity are thermally insulated. There are heated and cold parts, and these are placed on the bottom and top wall, respectively, whereas the remaining parts are thermally insulated. Design/methodology/approach The finite volume method is used to solve the dimensionless partial differential equations governing the problem. A comparison with previously published woks is presented and is found to be in an excellent agreement. Findings The minimization of entropy generation and local heat transfer according to different values of the governing parameters are presented in details. It is found that the presence of magnetic field has negative effects on the local entropy generation because of heat transfer and the local total entropy generation. Also, the increase in the heated part length leads to a decrease in the local Nusselt number. Originality/value This problem is original, as it has not been considered previously.